Brought to sickbay, Kirk, Spock and McCoy surmise the alien's skin coloration to be a mutation of some kind. The pilot is revived by Dr.McCoy and identifies himself as Lokai from the planet Cheron. Although grateful for the Enterprise's rescue, he is combative when Kirk questions him about the theft of the shuttlecraft. Kirk plans to return him to Starbase 4 to face serious theft charges once the important Arrianus mission is completed.

En route however, Chekov reports that sensors have detected a highly sophisticated (and invisible) vessel on an apparent collision course with the Enterprise. At the last moment before impact, the ship appears to disintegrate, but deposits its pilot on the bridge – similar in appearance to Lokai, but with his black and white skin colors reversed. "Explain, Spock," Kirk asks. "One of a kind?"

When Bele is brought to sickbay to see Lokai, the crew learns that Bele has been pursuing Lokai for a very long time: 50,000 Earth years as it turns out. Bele charges that Lokai led a revolt of people who are black on the left side against the ruling order, which is black on the right side. Lokai counters that the black/right (white/left) order enslaved the white/right (black/left) people of Cheron and continues to oppress them. Bele demands that Kirk surrender Lokai, while Lokai claims political asylum with the Federation. Kirk ends the bickering, giving Bele quarters and states his intention to fulfill his mission, then hand both of the aliens to Starbase 4 to have the matter settled. Bele is clearly not satisfied, but leaves sickbay. Kirk advises that Lokai get some rest, especially his vocal cords, as he will get a chance to practice his oratory when they arrive at Starbase 4.

Suddenly, the Enterprise is commandeered by an unknown source. Soon, Bele reveals on the bridge that he is controlling it, by using his mental powers to direct the ship to Cheron. Impervious to phasers, Kirk, along with Spock and Scotty, are forced to activate the three-part self-destruct sequence in order to force Bele to relinquish control of the ship.

With only six seconds left before the Enterprise destroys itself, Bele releases control of the starship. With force not being an option, both Bele and Lokai attempt to enlist the sympathies of the crew while en route to Ariannus, Lokai with the crew and Bele with Kirk and Spock. Kirk submits a report to Starfleet Command for a resolution.

Starfleet's answer to Bele's request is received while he speaks with Kirk and Spock--and it is to deny that request. Since Cheron has no diplomatic treaties with the Federation, Starfleet cannot extradite Lokai without due process. Uhura also adds that the decision from Starfleet notes that they are confident that Bele will be allowed to return to Cheron with Lokai after the hearing is over. Bele is pessimistic, however, believing that Lokai will again gain supporters in his cause and will escape from him again.

The Enterprise arrives at Ariannus and begins the decontamination procedures. Once the decontamination mission to Ariannus is complete, Kirk orders to head to Starbase 4, however, Bele sabotages the self-destruct mechanism as well as directional control, regains control of the ship, and re-forces it to head for Cheron again.

Lokai begs for the Enterprise crew to intervene, and Bele berates him, for he believes he has finally caught him. They fight, but Kirk tries to defuse the situation for fear of destroying the ship, saying the bridge will be their "last battlefield." Bele returns control, since their fighting will destroy themselves with the ship.

The crew realizes they are near Cheron, however, its sensors reveal massive destruction of all Cheron's major cities and huge piles of unburied corpses – the entire population of Cheron has apparently mutually annihilated itself in a civil war. Consumed with mutual insane hatred and blaming each other for the resulting holocaust, Bele and Lokai fight on the bridge, despite Kirk's offer for them to live with the Federation. Kirk implores them to give up their mutual hatred of one another, since that destroyed their planet and their people. Lokai derides Kirk, accusing him of being an "idealistic dreamer," and flees the bridge. The pair then chase each other through the ship's corridors, each eventually finding their way to the transporter room and returning to the planet's surface to continue their fight...the last two sapient life forms on a dead planet. Kirk sadly notes that, in the end, all they have left is their hatred of each other. Kirk decides to leave them there and orders that Sulu set course for Starbase 4.

"Captain's log, stardate 5730.2. The planet Ariannus is vital as a transfer point on regular space commercial lanes. It has been attacked by a bacterial invasion which threatens to render it lifeless unless checked. Our mission, to decontaminate it."

"Captain's log, stardate 5730.6. Having completed our mission to Ariannus, the Enterprise is now on course to Starbase 4. The crew is on normal routine and we are proceeding without incident."

"Captain's log, stardate 5730.7. In a deliberate act of sabotage, Commissioner Bele has burned out our destruct mechanism and, through the power of his will, has again taken over directional control of the Enterprise."

Curiously, the .6 entry is logged after the .7 entry. Bele sabotaged the Enterprise after the mission to Ariannus was completed.

"Mr. Spock, is this ship headed for Ariannus?"
"Negative, captain. The Enterprise is now moving in a circular course."
"And at warp 10 we're going nowhere mighty fast."

- Kirk, Spock and Scotty

"Disgusting is what I call them."

- Scott, on Bele and Lokai

"There was persecution on Earth once. I remember reading about it in my history class."
"Yes, but it happened way back in the twentieth century. There's no such primitive thinking today."

- Chekov and Sulu, trying to understand Cheron's civil war

"You're black on one side and white on the other."
"I am black on the right side."
"I fail to see the significant difference."
"Lokai is white on the right side. All of his people are white on the right side."

- Kirk and Bele

"Change is the essential process of all existence."

- Spock, to Bele

"I once heard that on some of your planets, people believe they are descended from apes."
"The actual theory is that all lifeforms evolved from the lower levels to the more advanced stages."

- Bele and Spock, on evolution

"Yes, he will delay, evade, and escape again. And in the process put thousands of innocent beings at each others throats, getting them to kill and maim, for a cause which they have no stake in. But, which he will force them to violently espouse by twisting their minds with his lies, his loathsome accusations, and his foul threats."

- Bele speaking about Lokai

"What do you do? Carry justice on your tongues? You will beg for it, but you won't fight or die for it!"
"After so many years of leading the fight, you seem very much alive."
"I doubt that the same can be said for many of his followers."

- Lokai pleading with Kirk and Spock to kill Bele

"You're finished, Lokai! Oh, we've got your kind penned in on Cheron into little districts, and it's not going to change! You've combed the galaxy, and come up with nothing but monocolored trash, do-gooders, and bleeding hearts.You're dead! You half-white!"
"You useless pieces of bland flesh! I'll take you with me! You half-black!"

- Bele and Lokai, before lunging at each other

"My people... all dead?"
"Yes, Commissioner. All of them."
"No one alive?"
"None at all, sir."

- Bele, Spock, Lokai, Spock

"You band of Murderers did this..."
"You Pyromaniacs"

- Bele, Lokai,

"Your planet is dead! There's nobody alive on Cheron because of hate. Listen to me. You both must end up dead if you don't stop hating."
"You're an idealistic dreamer."Bele. The chase is finished."
"He must not escape me!"
"Where can he go?"

- Kirk, Lokai, Kirk, Bele and Spock, after Lokai flees the ridge

"Shall I alert security, sir?"
"No, lieutenant. Where can they run?"

- Uhura and Kirk, after Lokai and Bele leave the bridge

"It doesn't make any sense."
"To expect sense from two mentalities of such extreme viewpoints, is not logical."
"But their planet's dead. Does it matter now which one of them was right?"
"Not to Lokai and Bele. All that matters to them is their hate."
"Do you suppose that's all they ever had, sir?"
"No... but that's all they have left."

The original story concept did not depict the aliens with bi-colored skin. Fred Freiberger recalled, "Gene [Coon] originally had a devil with a tail chasing an angel." (Captains' Logs: The Unauthorized Complete Trek Voyages, p. 74) Episode director Jud Taylor came up with the idea of bi-colored skin shortly before the episode began filming. His original suggestion was that they be half-black/half-white, one color from the waist up and the other from the waist down, but each wearing reversed color schemes. The central idea stuck but the colors were finally separated along the vertical axis rather than along the horizontal. (Inside Star Trek: The Real Story, pp. 399-400)

Producer Fred Freiberger stated that this was one of the episodes of which he was most proud.

Bele and Lokai both have brown hair on their heads, but their eyebrows are black and white to match their faces.

Nurse Chapel's only line in this episode is "He's coming around, doctor."

This episode represents the last on-screen appearance of the hangar deck in the original series. The shuttlecraft itself makes one last appearance on the planet set of "The Way to Eden".

Effects footage from "The Galileo Seven" was re-used for all of the original episode's shuttlecraft shots. As a result, despite dialogue stating that the shuttlecraft had been stolen from Starbase 4, the shuttlecraft tractor-beamed into the hangar deck was labeled Galileo NCC-1701/7. In the remastered version of the episode, the stolen shuttlecraft's front and sides markings were corrected to show Starbase 4 as its post. This CGI version of the shuttlecraft was labeled Da Vinci, after the noted Renaissance artist/scientist Leonardo da Vinci, and it had SB4-0314/2 as its new registry number.

Gene L. Coon's association with the series ended with the production of this episode. As with all of his contributions to the third season, for which he was unable to use his real name due to contractual obligations elsewhere, the story was credited to one of his pen names, Lee Cronin.

The reference bookInside Star Trek: The Real Story (pp. 197 & 399) attests that this episode was originally a first season story outline from August 1966, titled "Portrait in Black and White". The book additionally states that, by 1968, NBC and Paramount were keen on using every available story idea, so Coon's outline was "taken out of the trash bin" and Oliver Crawford based a teleplay on it. However, documentation from the making of TOS reveals that these two episodes actually were, from a production standpoint, significantly different. A first draft script of "Portrait in Black and White", never mentioned in the book, was issued on 28 September1966, and was entirely different from the storyline of "Let That Be Your Last Battlefield". (Gene Roddenberry Collection at UCLA, Box 19, Folder 10) They had different story numbers too – "Portrait in Black and White" was story #28, and "Let That Be Your Last Battlefield" was #93. Also, in the writers' report dated 29 March1968, the latter was listed as a new story assignment in progress, whereas the former had been listed among TOS' few shelved teleplays in the writers' report dated 1 March 1968. (Gene Roddenberry Collection at UCLA, Box 35, Folder 15)

This episode features a close-up of the Enterprise model. Zoom shots from below and above the saucer section are used, representing some of the rare 'beauty shots' of the ship filmed during the series (episodes "Operation -- Annihilate!" and "Metamorphosis" have unique shots of the Enterprise as well). During the opening credits in the first scene, for example, the camera glides underneath the saucer to an extreme closeup of the saucer's phaser section and light. "That Which Survives" uses the same shot briefly when the Enterprise is shaking at warp.

The self-destruct sequence from this episode is repeated exactly in Star Trek III: The Search for Spock; however, in Search for Spock, it is Scott who gives the second command in place of Spock, and Chekov who gives the third command instead of Scott. (The Star Trek Compendium 4th ed., p. 123) In this episode, the self-destruct is set for a 30-second countdown whereas the film has a sixty-second countdown.

The final chase scene depicting Lokai and Bele running through the corridors of the Enterprise is mixed with stock footage of burning cities filmed after WW II aerial bombing raids, as each visualizes the destruction of their shared home planet. Fred Freiberger stated, "We ran a little short on that show which is why it ended with a chase that went on forever. I thought it was a hell of a creative solution." (Captains' Logs: The Unauthorized Complete Trek Voyages, p. 74)

The Remastered version shows Cheron cities still burning from space.

Bele's totally "invisible" ship perhaps is the most noticeable effect of the biggest budget cut in the original series. (The Star Trek Compendium 4th ed., p. 123)

The episode's director, Jud Taylor, included a unique effect in this episode. During the "red alerts," the camera zoomed in and out quickly on the blinking red alert signal, and moreover, it was tilted at an angle. According to several sources, among them The Star Trek Compendium, this effect allegedly paid homage to Frank Gorshin's role as the Riddler in Batman, even though Taylor never directed any episodes of Batman.

In the third season blooper reel, several sequences from this episode are featured. In one, Frank Gorshin, who was also a talented impressionist, does a James Cagney imitation while on the transporter pad. In another, he and Lou Antonio collide forcefully as they are running through the corridors. (The Star Trek Compendium 4th ed., p. 123.) In yet another, Gorshin initially pronounces his character's name "Belly," before correcting himself and pronouncing it as it was pronounced in the finished episode. Finally, footage of nude swimmers in a pool was inserted at the point where Kirk asks, "Could it be a Romulan ship, using their cloaking device?"

In the 1970s, the Mego toy company created a "Cheron" action figure doll, but unlike both Bele and Lokai's makeup and costuming, the doll had no hair, and its costume was entirely half-black and half-white, right down to the boots.

The SciFi Channel, the DVD, and the remastered version added some new scenes that were not in the original and VHS version. After Kirk makes his first log entry at the beginning of this episode, he asks Chekov about estimated time to Ariannus, tells Uhura to contact them to tell them that decontamination is to begin on arrival, and asks Scott if it will it present any danger. Then after the shuttle is brought to the hangar deck, there is a shot of the shuttlecraft docking with the Enterprise. Sulu then calls Kirk in the turbolift to inform him that hangar doors are closed. Finally, there is a shot of Kirk and Spock in the hallway before they meet with the guards.

Several shots of the main viewer from the rear of the bridge are recycled shots that show Hadley in Chekov's position, but we hear Chekov's voice and see him in the closeup.